[AMBER] Problem with mdnab: ERROR in RATTLE

From: Andrey <aland.parallels.mipt.ru>
Date: Fri, 13 Apr 2012 23:57:19 +0400


I'm new to Amber, and I'm trying to perform an MMPBSA simulation with

I've prepared a set of protein-peptide complexes, and run minimization
on them with minab, after creating parameters with pytleap (ff03.r1
minab "../../build/amber/$prefix.leap.pdb"
"../../build/amber/$prefix.leap.prm" "./pdb/$prefix.pdb" 2 5000 #
$prefix points to one of the complexes in question.
I runs perfectly fine:
initial energy: -7253.479 kcal/mol
final energy: -7285.521 kcal/mol
minimizer finished after 4925 iterations
refined coordinates written to ./pdb/cdk6_p6_3_cplx.pdb

However, when I try to run subsequent equilibrium with mdnab, for 2 of 8
complexes I encounter the following error:
  mdnab "../min/pdb/${PREFIX}.pdb"
"../../build/amber/${PREFIX}.leap.prm" "traj/${PREFIX}" 2 500
Reading parm file (../../build/amber/cdk6_p6_3_cplx.leap.prm)
         mm_options: cut=12.000000
         mm_options: nsnb=25
         mm_options: diel=C
         mm_options: gb=2
         mm_options: rgbmax=12.000000
         mm_options: rattle=1
         mm_options: dt=0.002000
         mm_options: ntpr=101
         mm_options: ntpr_md=10
         mm_options: ntwx=0
         mm_options: zerov=0
         mm_options: tempi=50.000000
         mm_options: temp0=100.000000
         mm_options: gamma_ln=20.000000
         mm_options: wcons=0.000000
       iter Total bad vdW elect nonpolar
genBorn frms
ff: 0 -7285.90 4577.15 -1029.51 -6770.49 0.00 -4063.05
md: 1 0.002 -nan -nan -nan -nan
md: 10 0.020 -nan nan -nan -nan
[and so on]

For other complexes besides these two (even the ones with the same
peptide, but another binding point) mdnab finishes successfully.

If I set rattle=0, everything is ok, but I suspect that trajectories
without RATTLE could not be directly compared with RATTLEd trajectories.
I've tried running first stage of heating without RATTLE, and switch it
on for subsequent stages, but again, as soon as RATTLE is enabled,
simulation fails.
Searching the web I've found only suggestions to minimize the system
better, but when I try to minimize already minimized structure, the
process stops after ~20 steps, and does not affect behavior of mdnab.

I'm using the latest release of AmberTools, with recent patch (Author:
Jason Swails, Date: Apr. 10, 2012).

Thanks in advance,

Andrey Alekseenko
Moscow Institute of Physics and Technology

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Received on Fri Apr 13 2012 - 13:00:04 PDT
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